crossing96/oncoscreening huggingface dataset:
RNA Expression Profiling of Lymphoepithelioma-Like Carcinoma of the Bladder Reveals a Basal-Like Molecular Subtype.	Lymphoepithelioma-like carcinoma of the bladder (LELC-B) is a rare subtype of urothelial carcinoma consisting of undifferentiated epithelial cells within a dense inflammatory cell infiltrate. We set out to molecularly characterize LELC-B through RNA expression profiling as well as immunohistochemistry (IHC) to understand its underlying biology. Sixteen cases of LELC-B were identified at Johns Hopkins University. RNA sequencing was performed on 14 cases. IHC staining for programmed cell death ligand 1 (PD-L1) and mismatch repair proteins MutL homolog 1 (MLH1), MutS homolog 2 (MSH2), MSH6, and PMS1 homolog, mismatch repair system component 2 (PMS2) was performed. Transcriptomic profiling of LELC-B showed that they are enriched in a basal-like phenotype, with 12 of 14 LELC-B cases correlating to the basal centroid of the bladder cancer analysis of subtypes by gene expression 47 (BASE47) predictive analysis of microarrays (PAM) classifier. Gene signature analysis confirmed the lymphocyte infiltration profile consistent with the histomorphology. LELC-B lacked features to explain the robust lymphocytic infiltrate, such as loss of mismatch repair protein expression or expression of Epstein-Barr virus transcripts. Nonetheless, PD-L1 IHC was positive in 93% of LELC cases. Our study demonstrates that LELC-B tumors are enriched in a basal-like molecular subtype and share a high level of immune infiltration and PD-L1 expression, similar to basal tumors. The basal-like phenotype is consistent with the known sensitivity of LELC-B to chemotherapy and suggests that immune checkpoint therapy should be explored in this rare disease.	bladder
Use and Validation of the AUA/SUO Risk Grouping for Nonmuscle Invasive Bladder Cancer in a Contemporary Cohort.	PURPOSE: We applied nonmuscle invasive bladder cancer AUA (American Urological Association)/SUO (Society of Urologic Oncology) guidelines for risk stratification and analyzed predictors of recurrence and progression. MATERIALS AND METHODS: We retrospectively reviewed the records of 398 patients with nonmuscle invasive bladder cancer treated between 2001 and 2017. Descriptive statistics were used to compare AUA/SUO risk groups. Predictors of recurrence and progression were determined by multivariable regression. Kaplan-Meier analysis was done, a Cox proportional hazards regression model was created and time dependent AUCs were calculated to determine progression-free and recurrence-free survival by risk group. RESULTS: Median followup was 37 months (95% CI 35-42). Of the patients 92% underwent bacillus Calmette-Guérin induction and 46% received at least 1 course of maintenance treatment. Of the patients 11.5% were at low, 32.5% were at intermediate and 55.8% were at high risk. In patients at low, intermediate and high risk the 5-year progression-free survival rate was 93%, 74% and 54%, and the 5-year recurrence-free survival rate was 43%, 33% and 23%, respectively. Kaplan-Meier analysis was done to stratify high grade Ta 3 cm or less tumor recurrence-free and progression-free survival in the intermediate vs the high risk group. Relative to low risk, classification as intermediate and as high risk was an independent predictor of progression (HR 9.7, 95% CI 2.23-42.0, p <0.01, and HR 36, 95% CI 8.16-159, p <0.001, respectively). Recurrence was more likely in patients at high risk than in those at low risk (HR 2.03, 95% CI 1.11-3.71, p=0.022). For recurrence and progression the 1-year AUC was 0.60 (95% CI 0.546-0.656) and 0.68 (95% CI 0.622-0.732), respectively. CONCLUSIONS: The AUA/SUO nonmuscle invasive bladder cancer risk classification system appropriately stratifies patients based on the likelihood of recurrence and progression. It should be used at diagnosis to counsel patients and guide therapy.	bladder
Liquid biopsy in the clinical management of bladder cancer: current status and future developments.	Introduction: The use of liquid biopsy on the blood from solid malignancies provides a convenient way of detecting actionable mutations, monitoring treatment response, detecting early recurrence and prognosticating outcomes. The aim of this review is to discuss the current status and future direction of serum biomarkers in the clinical management of urinary bladder cancer.Areas covered: This review provides an overview of blood liquid biopsy and bladder cancer using methods of circulating tumors cells, circulating RNA, serum metabolites and cell-free DNA. Recent clinical studies and advances in methodology are emphasized. We performed a literature search using PMC/PubMed with keywords including 'liquid biopsy', 'circulating tumor DNA', 'cell-free DNA', 'biomarkers', 'bladder cancer' 'precision medicine'. Additional articles were obtained from the cited references of key articles. An emphasis was placed on recent studies published since 2018.Expert opinion: Liquid biopsies represent a potential biomarker using cell-free DNA, metabolomic profiles of altered cellular metabolism, circulating cancer cells and RNA. Despite displaying tremendous clinical promise, the current status of the blood liquid biopsies has not reached fruition. However, future investigations should lead the evolution of liquid biomarker into clinical utility for the management of bladder cancer.	bladder
The significance of calprotectin, CD147, APOA4 and DJ-1 in non-invasive detection of urinary bladder carcinoma.	Aim of the study is to define the diagnostic accuracy of selected urinary protein biomarkers in the non-invasive detection of primary and recurrent urothelial carcinoma of the urinary bladder. The urinary levels of calprotectin, CD147, APOA4 and protein deglycase DJ-1 were examined in 255 individuals, including 60 controls with non-malignant urological disease, 61 patients with a history of urinary bladder cancer with negative cytology and negative cystoscopy and 134 patients with urinary bladder cancer. Urinary concentrations of biomarkers were determined by Enzyme-Linked Immunosorbent Assay (ELISA). During the follow-up of patients with non-muscle invasive bladder cancer (NMIBC), a group of 44 patients with cancer recurrence was compared to the group of 61 patients with a history of NMIBC but with no evidence of disease. Urinary concentrations of the evaluated markers did not reveal any significant difference between these groups. During the primary diagnosis, a group of 90 patients with primary bladder cancer and 60 subjects with benign disease were compared. Urinary levels of CD147 were not significantly higher in patients with tumors. The greatest diagnostic accuracy was observed in APOA4 (sensitivity 55.6, specificity 83.3, AUC 0.75), and lesser in calprotectin (sensitivity 39.4, specificity 87.7, AUC 0.66) and in DJ-1 (sensitivity 61.1, specificity 66.7, AUC 0.64), respectively. Apolipoprotein A4 may be used potentially as a supplemental urinary marker in the diagnosis of primary bladder cancer.	bladder
Pparg promotes differentiation and regulates mitochondrial gene expression in bladder epithelial cells.	The urothelium is an epithelial barrier lining the bladder that protects against infection, fluid exchange and damage from toxins. The nuclear receptor Pparg promotes urothelial differentiation in vitro, and Pparg mutations are associated with bladder cancer. However, the function of Pparg in the healthy urothelium is unknown. Here we show that Pparg is critical in urothelial cells for mitochondrial biogenesis, cellular differentiation and regulation of inflammation in response to urinary tract infection (UTI). Superficial cells, which are critical for maintaining the urothelial barrier, fail to mature in Pparg mutants and basal cells undergo squamous-like differentiation. Pparg mutants display persistent inflammation after UTI, and Nf-KB, which is transiently activated in response to infection in the wild type urothelium, persists for months. Our observations suggest that in addition to its known roles in adipogegnesis and macrophage differentiation, that Pparg-dependent transcription plays a role in the urothelium controlling mitochondrial function development and regeneration.	bladder
High aurora kinase expression identifies patients with muscle-invasive bladder cancer who have poor survival after neoadjuvant chemotherapy.	OBJECTIVES: Overexpression of aurora kinase A (AURKA) confers a poor prognosis in patients with urothelial carcinoma of the bladder. The prognostic value of high aurora kinase B (AURKB) expression in local bladder cancer is not well defined, and whether the prognostic value of either AURKA or AURKB is affected by the use of chemotherapy is unknown. We sought to characterize the impact of high AURKA and AURKB expression on clinical outcome in patients with muscle-invasive bladder cancer (MIBC) who received neoadjuvant chemotherapy (NAC). MATERIALS AND METHODS: Immunohistochemistry for AURKA and AURKB was performed on pretreatment diagnostic transurethral resection of bladder tumor (TURBT) and matched cystectomy specimens in 50 subjects with MIBC who received NAC. Receiver operator characteristic curves (ROC) were calculated to assess the impact of AURKA and AURKB expression on pathologic response rate. Kaplan-Meier techniques and Cox proportional hazards models were used to assess the association with relapse-free survival (RFS) and overall survival (OS). RESULTS: Twenty-two of 50 [44%] patients had residual muscle-invasive (ypT2-4) urothelial carcinoma after NAC. Neither baseline tumor expression of AURKA (ROC = 0.57, P = 0.46) nor AURKB (ROC = 0.56, P = 0.87) predicted for ypT2-4 status. However, baseline expression of AURKA above the 75th percentile for this cohort was associated with an inferior RFS, (HR = 3.88, P = 0.008) and OS, (HR = 6.10, P < 0.001). Similar trends for worse survival outcomes were also observed for high AURKB levels (RFS, [HR = 2.2, P = 0.13] and OS, (HR = 2.25, P = 0.09). CONCLUSIONS: High baseline tumor AURKA and AURKB expression identified MIBC patients with inferior RFS and OS despite the use of NAC and may identify patients who should be prioritized for clinical trial enrollment rather than standard cisplatin-based chemotherapy.	bladder
Exosomal long noncoding RNA LNMAT2 promotes lymphatic metastasis in bladder cancer.	Patients with bladder cancer (BCa) with clinical lymph node (LN) metastasis have an extremely poor prognosis. VEGF-C has been demonstrated to play vital roles in LN metastasis in BCa. However, approximately 20% of BCa with LN metastasis exhibits low VEGF-C expression, suggesting a VEGF-C-independent mechanism for LN metastasis of BCa. Herein, we demonstrate that BCa cell-secreted exosome-mediated lymphangiogenesis promoted LN metastasis in BCa in a VEGF-C-independent manner. We identified an exosomal long noncoding RNA (lncRNA), termed lymph node metastasis-associated transcript 2 (LNMAT2), that stimulated human lymphatic endothelial cell (HLEC) tube formation and migration in vitro and enhanced tumor lymphangiogenesis and LN metastasis in vivo. Mechanistically, LNMAT2 was loaded to BCa cell-secreted exosomes by directly interacting with heterogeneous nuclear ribonucleoprotein A2B1 (hnRNPA2B1). Subsequently, exosomal LNMAT2 was internalized by HLECs and epigenetically upregulated prospero homeobox 1 (PROX1) expression by recruitment of hnRNPA2B1 and increasing the H3K4 trimethylation level in the PROX1 promoter, ultimately resulting in lymphangiogenesis and lymphatic metastasis. Therefore, our findings highlight a VEGF-C-independent mechanism of exosomal lncRNA-mediated LN metastasis and identify LNMAT2 as a therapeutic target for LN metastasis in BCa.	bladder
Glycemic impact of a diet and lifestyle intervention on diabetics and prediabetics during treatment for non-muscle invasive bladder cancer.	Introduction: Patients with Type II Diabetes Mellitus (DM2) have increased risk of recurrence and progression of non-muscle invasive bladder cancer (NMIBC). Glucose control through lifestyle intervention is an uninvestigated, attractive strategy to decrease risk of cancer recurrence. We test the feasibility of a diet and exercise program and its glycemic impact in patients with DM2 and NMIBC.Materials/methods: Five participants with NMIBC and pre-diabetes or DM2 were recruited for a pilot, prospective clinical trial. Each participant received dietary counseling for 16 sessions during clinical visits. The intervention included a carbohydrate-restricted (CR) diet (<130 grams per day), 30 min, walking 5×/wk, and 5000 steps daily. Diet compliance was measured with 24-hour diet recall. Exercise was monitored with accelerometer and self-report.Results: Five participants enrolled and two participants completed the 12-month intervention. Adherence was 60% to CR diet and 84% to exercise goals. Participants reduced carbohydrate consumption by 44%. Participants showed reductions in fasting blood glucose, HbA1c, glucosuria, fasting blood insulin, and body weight, and increased euglycemia on continuous glucose monitoring.Conclusions: Adherence to a CR diet and exercise goals is feasible in patients with NMIBC and DM2 and also leads improved glucose control. A phase-II trial on bladder cancer-specific outcomes is warranted.	bladder
Benzyl isothiocyanate promotes miR-99a expression through ERK/AP-1-dependent pathway in bladder cancer cells.	Benzyl isothiocyanate (BITC), a bioactive natural product present in cruciferous vegetables, has been proved to prevent cancer progression through various mechanisms. In our previous report, we proved that BITC exhibits antitumor effects in bladder cancer by suppressing IGF1R, FGFR3, and mTOR, which is mediated by miR-99a expression. In this study, we identified the signal pathway involved in regulating miR-99a expression after BITC exposure in bladder cancer. Treatment with different BITC concentrations resulted in induction of miR-99a expression in bladder cancer cell lines. Activation of extracellular signal-regulated protein kinase (ERK) and c-jun N-terminal kinase was observed in bladder cancer after BITC treatment for 24 hours. Interestingly, by using a chemical inhibitor of candidate pathways, we found that only the ERK signal pathway is required for miR-99a expression. Furthermore, we evaluated the transcription factor that may contribute to miR-99a expression in response to BITC treatment. The results indicated that c-Jun/AP-1 was activated after BITC treatment. Moreover, we confirmed c-Jun/AP-1 activation through immunofluorescence and the luciferase reporter assay. The results showed that BITC treatment markedly improved nuclear translocation of c-Jun/AP-1 and luciferase activity dose dependently. Finally, pretreatment with the ERK inhibitor U0126 diminished c-Jun phosphorylation and transcriptional activation, suggesting that BITC elicits ERK/c-Jun signal transduction, which is responsible for miR-99a expression in bladder cancer. The present work identifies the mechanism involved in upregulation miR-99a after BITC treatment, which provides an explanation for BITC biological function in our previous work.	bladder
Embracing study heterogeneity for finding genetic interactions in large-scale research consortia.	Genetic interactions have been recognized as a potentially important contributor to the heritability of complex diseases. Nevertheless, due to small effect sizes and stringent multiple-testing correction, identifying genetic interactions in complex diseases is particularly challenging. To address the above challenges, many genomic research initiatives collaborate to form large-scale consortia and develop open access to enable sharing of genome-wide association study (GWAS) data. Despite the perceived benefits of data sharing from large consortia, a number of practical issues have arisen, such as privacy concerns on individual genomic information and heterogeneous data sources from distributed GWAS databases. In the context of large consortia, we demonstrate that the heterogeneously appearing marginal effects over distributed GWAS databases can offer new insights into genetic interactions for which conventional methods have had limited success. In this paper, we develop a novel two-stage testing procedure, named phylogenY-based effect-size tests for interactions using first 2 moments (YETI2), to detect genetic interactions through both pooled marginal effects, in terms of averaging site-specific marginal effects, and heterogeneity in marginal effects across sites, using a meta-analytic framework. YETI2 can not only be applied to large consortia without shared personal information but also can be used to leverage underlying heterogeneity in marginal effects to prioritize potential genetic interactions. We investigate the performance of YETI2 through simulation studies and apply YETI2 to bladder cancer data from dbGaP.	bladder
Variation in energy metabolism arising from the effect of the tumor microenvironment on cell biological behaviors of bladder cancer cells and endothelial cells.	Tumor energy metabolism and angiogenesis play significant roles in tumor genesis and development, while the effect of the tumor microenvironment (TME), which tumors rely on, is always ignored. In this research, we cocultured bladder cancer (BC) T24 cells with tumor-associated human umbilical vein endothelial cells (HUVECs) under normoxic and hypoxic conditions and detected proliferation, migration, oxidative phosphorylation (OXPHOS) and glycolysis to reveal the energy metabolism characteristics and their effect on cell biological behaviors (CBBs) in the TME. Compared with single-cultured cells, both cocultured T24 cells and HUVECs showed poor proliferation and migration in hypoxic environment, and OXPHOS was activated in cocultured T24 cells but weakened in cocultured HUVECs. However, in normoxic environment, cocultured T24 cells grew much faster while cocultured HUVECs grew slower compared with single-cultured cells. Additionally, glycolysis played a crucial role in energy metabolism and was inhibited in cocultured T24 cells but activated in cocultured HUVECs. In normoxic TME, OXPHOS take main responsibility of energy metabolism. T24 cells exhibited increased proliferation and migration with HUVECs support. In hypoxic TME, glycolysis may be the primary energy supply pathway. T24 cells then exhibit suppressed proliferation and migration, while HUVECs tend to promote angiogenesis to adapt to the harsh TME.	bladder
Large Single Institution Comparison of Perioperative Outcomes and Complications of Open Radical Cystectomy, Intracorporeal Robot-Assisted Radical Cystectomy and Robotic Extracorporeal Approach.	PURPOSE: Bladder cancer management options include open radical cystectomy and robot-assisted radical cystectomy with intracorporeal or extracorporeal urinary diversion. The existing literature shows no difference in the major complication rate between open radical cystectomy and extracorporeal urinary diversion. However, the emerging popularity of intracorporeal urinary diversion has exposed the need to compare a completely intracorporeal method to alternative approaches. To our knowledge the robotic intracorporeal advantage regarding major complications has not yet been established in an evaluation of all 3 modalities. We compared outcomes and complications of open, intracorporeal and extracorporeal cystectomy techniques at a high volume institution. MATERIALS AND METHODS: We queried a prospectively maintained database for patients who underwent radical cystectomy from 2011 to 2018 for an oncologic indication. Perioperative and pathological outcomes, and 30 and 90-day major complications were assessed. Statistical analyses were done using the Pearson chi-square, Kruskal-Wallis and Kaplan-Meier tests, and multivariable regression. RESULTS: A total of 948 patients met the study criteria, including 272, 301 and 375 treated with open radical cystectomy, intracorporeal urinary diversion and extracorporeal urinary diversion, respectively. Median followup was 26 months. Intracorporeal urinary diversion cases had lower estimated blood loss (p <0.001), shorter hospitalization (p <0.001) and a lower ileus rate (p=0.023) than extracorporeal urinary diversion and open radical cystectomy cases. Importantly, intracorporeal urinary diversion was associated with lower 30 and 90-day major complication rates vs extracorporeal urinary diversion and open radical cystectomy (90-day Clavien-Dindo III-V 16.9% vs 24.8% and 26.1%, respectively, p=0.015). There was no significant difference in the readmission rate according to the surgical approach. Multivariable predictors of increased 90-day major complications were patient age, the Charlson Comorbidity Index and operative time. On multivariable analysis intracorporeal urinary diversion was associated with reduced 90-day major complications (OR 0.58, p=0.037). CONCLUSIONS: In a 3-way comparison intracorporeal urinary diversion demonstrated a lower major complication rate and perioperative benefits compared to extracorporeal urinary diversion and open radical cystectomy.	bladder
[ICG lymphography and fluorescence in pelvic lymphadenectomy for bladder and prostate cancer.].	OBJECTIVE: ICG navigation in cancer surgery may help during pelvic lymphadenectomy. METHODS: We performed a systematic review combining the terms: bladder cancer or radical cystectomy and ICG, and prostate cancer or radical prostatectomy and ICG. We used the PRISMA guidelines recommendations. We describe the populations studied in each work, the pathological results, as well as the parameters specificity, sensitivity and predictive values. RESULTS: In muscle-invasive bladder cancer, 4 case series analyzed the performance of lymphography with ICG. The most accepted injection method is under endoscopic vision. Several punctures are done in the submucosa and the detrusor surrounding the scar. Sentinel nodes were found in up to 92% of patients with a technique sensitivity to find metastases of 88% in the series with largest casuistry. In prostate cancer, we collected data from 11 case series. Nine of them apply transrectal or transperineal dilution immediately before surgery. Sensitivity in the detection of all adenopathies ranged between 44% and 100%. The sensitivity of the technique to know the lymph node stage ranges between 67% and 100%. CONCLUSIONS: There is little experience of ICG-guided lymph node dissedction in bladder tumors. Endoscopic fluorophore injection allows us to find the nodes that drain the infiltrated area. However, the use of this technique is not widespread. In prostate cancer, it is a reproducible and efficient technique for staging patients with prostate cancer.	bladder